def get_sample_rot_distr():
# create materials
substrate_material = ba.HomogeneousMaterial("Substrate", 6.05878e-6,
6.94321e-11)
particle_material = ba.HomogeneousMaterial("ParticleCore", -0.609e-6,
0.183e-6)
layer_material = ba.HomogeneousMaterial("D2O", 1.85762e-5, 3.31309e-11)
# create mesocrystal
# lattice
lat = create_hex_lattice(distance, length)
# basis particle
ff = ba.FormFactorCylinder(radius, length)
particle = ba.Particle(particle_material, ff)
# rotate cylinder to make it parallel to the substrate
rotation = ba.RotationY(90.0 * ba.degree)
particle.setRotation(rotation)
basis = ba.ParticleComposition(particle)
# mesocrystal
total_height = nbr_layers * distance * np.sin(hex_angle)
# using a Gaussian form factor as the overall shape of where the cylinders are
meso_ff = ba.FormFactorGauss(meso_width, total_height)
# assemble them into mesocrystal
npc = ba.Crystal(basis, lat)
dw_factor = 0.2
npc.setDWFactor(dw_factor)
meso = ba.MesoCrystal(npc, meso_ff)
# rotate mesocrystal
rot_y = ba.RotationY(180.0 * ba.degree)
meso.setRotation(rot_y) # turn upside down
rot_z = ba.RotationZ(0.1 * ba.degree)
meso.applyRotation(rot_z) # rotate around Z
meso.setPosition(0.0, 0.0, 0.0)
# add uniform distribution of the domain orientations
rot_distr = ba.DistributionGate((90.0 - rz_range) * ba.degree,
(90.0 + rz_range) * ba.degree)
ang_distr = ba.ParameterDistribution("*MesoCrystal/EulerRotation/Gamma",
rot_distr, rz_num)
part_coll = ba.ParticleDistribution(meso, ang_distr)
# Create multilayer
multi_layer = ba.MultiLayer()
d2o_layer = ba.Layer(layer_material)
substrate_layer = ba.Layer(substrate_material)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(part_coll)
d2o_layer.addLayout(particle_layout)
# the sample is upside down
multi_layer.addLayer(substrate_layer)
multi_layer.addLayer(d2o_layer)
return multi_layer
def testBoxTransform(self):
"""
Reference box of (10,50,20) size is compared against the box (50,20,10) with two rotations applied to get
reference one
"""
mParticle = ba.HomogeneousMaterial("Ag", 1.245e-5, 5.419e-7)
# reference box
length = 10
width = 50
height = 20
box = ba.Particle(mParticle, ba.FormFactorBox(length, width, height))
box.setPosition(kvector_t(0, 0, -layer_thickness / 2 - height / 2))
reference_data = self.get_result(box)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_TransformBox.int")
# second box
length = 50
width = 20
height = 10
box = ba.Particle(mParticle, ba.FormFactorBox(length, width, height))
box.setRotation(ba.RotationZ(90 * deg))
box.rotate(ba.RotationY(90 * deg))
box.setPosition(kvector_t(0, 0, -layer_thickness / 2))
data = self.get_result(box)
diff = ba.RelativeDifference(data, reference_data)
print(diff)
self.assertLess(diff, 1e-10)
def get_sample():
# Defining Materials
material_1 = ba.HomogeneousMaterial("Air", 0.0, 0.0)
material_2 = ba.HomogeneousMaterial("Au", 3.53665637e-05,
2.9383311e-06)
material_3 = ba.HomogeneousMaterial("Si", 5.73327e-06, 1.006366e-07)
# Defining Layers
layer_1 = ba.Layer(material_1)
layer_2 = ba.Layer(material_3)
# Defining Form Factors
formFactor_1 = ba.FormFactorTruncatedSphere(159.0 * nm, 244.0 * nm,
0.0 * nm)
# Defining Particles
particle_1 = ba.Particle(material_2, formFactor_1)
particle_1_rotation = ba.RotationY(60.0 * deg)
particle_1.setRotation(particle_1_rotation)
particle_1_position = kvector_t(0.0 * nm, 0.0 * nm, 439.0 * nm)
particle_1.setPosition(particle_1_position)
# Defining composition of particles at specific positions
z1 = j
z2 = j + 120
z3 = j + 240
particleComposition_1 = ba.ParticleComposition()
particleComposition_1.addParticle(particle_1)
particleComposition_1_rotation = ba.RotationZ(z1 * deg)
particleComposition_1.setRotation(particleComposition_1_rotation)
particleComposition_2 = ba.ParticleComposition()
particleComposition_2.addParticle(particle_1)
particleComposition_2_rotation = ba.RotationZ(z2 * deg)
particleComposition_2.setRotation(particleComposition_2_rotation)
particleComposition_3 = ba.ParticleComposition()
particleComposition_3.addParticle(particle_1)
particleComposition_3_rotation = ba.RotationZ(z3 * deg)
particleComposition_3.setRotation(particleComposition_3_rotation)
# Defining Particle Layouts and adding Particles
layout_1 = ba.ParticleLayout()
layout_1.addParticle(particleComposition_1, 1.0)
layout_1.addParticle(particleComposition_2, 1.0)
layout_1.addParticle(particleComposition_3, 1.0)
layout_1.setTotalParticleSurfaceDensity(0.001)
# Adding layouts to layers
layer_1.addLayout(layout_1)
# Defining Multilayers
multiLayer_1 = ba.MultiLayer()
multiLayer_1.addLayer(layer_1)
multiLayer_1.addLayer(layer_2)
return multiLayer_1
def get_sample():
# Defining Materials
material_1 = ba.HomogeneousMaterial("example01_Air", 0.0, 0.0)
material_2 = ba.HomogeneousMaterial("Si", 5.73327e-06, 1.006366e-07)
# Defining Layers
layer_1 = ba.Layer(material_1)
layer_2 = ba.Layer(material_2)
particleComposition_1 = ba.ParticleComposition()
for i in range(nslices):
r = 159 * nm - i * 2
z = i * 15 * nm
y = z + 15 * nm
# Defining Form Factors
formFactor_1 = ba.FormFactorCone6(r, 5.0 * nm, 68.0 * deg)
formFactor_2 = ba.FormFactorCone6(r, 10.0 * nm, 78.0 * deg)
# Defining Particles
particle_1 = ba.Particle(material_2, formFactor_1)
particle_1_rotation = ba.RotationY(180.0 * deg)
particle_1.setRotation(particle_1_rotation)
particle_1_position = kvector_t(0.0 * nm, 0.0 * nm, y * nm)
particle_1.setPosition(particle_1_position)
particle_2 = ba.Particle(material_2, formFactor_2)
particle_2_position = kvector_t(0.0 * nm, 0.0 * nm, z * nm)
particle_2.setPosition(particle_2_position)
# Defining composition of particles at specific positions
particleComposition_1.addParticle(particle_1)
particleComposition_1.addParticle(particle_2)
particleComposition_1_rotation = ba.RotationZ(j * deg)
particleComposition_1.setRotation(particleComposition_1_rotation)
# Defining Particle Layouts and adding Particles
layout_1 = ba.ParticleLayout()
layout_1.addParticle(particleComposition_1, 1.0)
layout_1.setTotalParticleSurfaceDensity(0.001)
# Adding layouts to layers
layer_1.addLayout(layout_1)
# Defining Multilayers
multiLayer_1 = ba.MultiLayer()
multiLayer_1.addLayer(layer_1)
multiLayer_1.addLayer(layer_2)
return multiLayer_1
def get_sample():
"""
Returns a sample
"""
# defining materials
m_si = ba.MaterialBySLD("Si", sld_Si, sld_Si_im)
m_d2o = ba.MaterialBySLD("D2O", sld_D2O, sld_D2O_im)
m_core = ba.MaterialBySLD("Me3O5:D2O2", 2.0 * 1.0e-06, 0.0)
m_shell = ba.MaterialBySLD("Me3O5:D2O", 3.9 * 1.0e-06, 0.0)
# layer with particles
# calculate average SLD
Vcore = vol(core_radius, core_height)
Vshell = vol(radius, height) - Vcore
f_d2o = 0.7
f_core = (1.0 - f_d2o) / (1 + Vshell / Vcore)
f_shell = (1.0 - f_d2o) / (1 + Vcore / Vshell)
sld_mix = f_d2o * sld_D2O + f_shell * 3.9 * 1.0e-06 + f_core * 2.0 * 1.0e-06
m_mix = ba.MaterialBySLD("mix", sld_mix, 0.0)
# fluctuation component
ff_microgel = FormFactorMicrogel(b, xi, xiz)
microgel = ba.Particle(m_core, ff_microgel)
microgel_layout = ba.ParticleLayout()
microgel_layout.addParticle(microgel, 1.0)
# collection of particles
ff = ba.FormFactorTruncatedSphere(radius=radius, height=height)
ff_core = ba.FormFactorTruncatedSphere(radius=core_radius,
height=core_height)
transform = ba.RotationY(180.0 * deg)
shell_particle = ba.Particle(m_shell, ff)
core_particle = ba.Particle(m_core, ff_core)
core_position = ba.kvector_t(0.0, 0.0, 0.0)
particle = ba.ParticleCoreShell(shell_particle, core_particle,
core_position)
particle.setPosition(ba.kvector_t(0.0, 0.0, 0.0))
particle.setRotation(transform)
nparticles = 2 # the larger is this number, the more slow will be the simulation. 10 is usually enough
sigma = 0.2 * radius
gauss_distr = ba.DistributionGaussian(radius, sigma)
sigma_factor = 2.0
par_distr = ba.ParameterDistribution(
"/ParticleCoreShell/Particle1/TruncatedSphere/Radius",
gauss_distr, nparticles, sigma_factor,
ba.RealLimits.lowerLimited(core_radius + 1.0))
par_distr.linkParameter(
"/ParticleCoreShell/Particle1/TruncatedSphere/Height")
par_distr.linkParameter(
"/ParticleCoreShell/Particle0/TruncatedSphere/Height")
par_distr.linkParameter(
"/ParticleCoreShell/Particle0/TruncatedSphere/Radius")
part_coll = ba.ParticleDistribution(particle, par_distr)
microgel_layout.addParticle(part_coll, 1.2e-05)
# interference can be neglected
interference = ba.InterferenceFunctionNone()
microgel_layout.setInterferenceFunction(interference)
# describe layer roughness
roughness = ba.LayerRoughness()
roughness.setSigma(1.2 * ba.nm)
roughness.setHurstParameter(0.8)
roughness.setLatteralCorrLength(570.0 * ba.nm)
# create layers
d2o_layer = ba.Layer(m_d2o)
mix_layer = ba.Layer(m_mix, 2.0 * height)
mix_layer.addLayout(microgel_layout)
si_layer = ba.Layer(m_si)
multi_layer = ba.MultiLayer()
multi_layer.addLayer(si_layer)
multi_layer.addLayer(mix_layer)
multi_layer.addLayerWithTopRoughness(d2o_layer, roughness)
return multi_layer
""" Plot form factors. """ import bornagain as ba from bornagain import nanometer, degree import bornplot as bp import math det = bp.Detector(200, -5, 5, -5, 5) n = 3 results = [] edge = 3.2 title = 'face normal' trafo = ba.RotationY(26.5651 * degree) ff = ba.FormFactorDodecahedron(edge * nanometer) data = bp.run_simulation(det, ff, trafo) results.append(bp.Result(0, data, title)) title = 'vertex normal' trafo = ba.RotationY(-52.6226 * degree) ff = ba.FormFactorDodecahedron(edge * nanometer) data = bp.run_simulation(det, ff, trafo) results.append(bp.Result(1, data, title)) title = 'edge normal' trafo = ba.RotationY(58.2825 * degree) ff = ba.FormFactorDodecahedron(edge * nanometer) data = bp.run_simulation(det, ff, trafo) results.append(bp.Result(2, data, title))
"""
Plot form factor.
"""
import bornagain as ba
from bornagain import nanometer, degree
import bornplot as bp
det = bp.Detector(200, 0, 5, 0, 5)
n = 4
results = []
for i in range(n):
theta = 30 * i / (n - 1)
title = r'$\vartheta=%d^\circ$' % theta
ff = ba.FormFactorTruncatedSphere(4.2 * nanometer, 6.1 * nanometer)
trafo = ba.RotationY(theta * degree)
data = bp.run_simulation(det, ff, trafo)
results.append(bp.Result(i, data, title))
bp.make_plot(results, det, "ff_TruncatedSphere")
""" Plot form factors. """ import bornagain as ba from bornagain import nanometer, degree import bornplot as bp import math det = bp.Detector( 200, -5, 5, -5, 5 ) n = 3 results = [] edge = 4.8 title = 'face normal' trafo = ba.RotationY(48.1897*degree) ff = ba.FormFactorIcosahedron(edge*nanometer) data = bp.run_simulation(det,ff,trafo) results.append( bp.Result(0, data, title) ) title = 'vertex normal' trafo = ba.RotationY(-52.6226*degree) ff = ba.FormFactorIcosahedron(edge*nanometer) data = bp.run_simulation(det,ff,trafo) results.append( bp.Result(1, data, title) ) title = 'edge normal' trafo = ba.RotationY(69.0948*degree) ff = ba.FormFactorIcosahedron(edge*nanometer) data = bp.run_simulation(det,ff,trafo) results.append( bp.Result(2, data, title) )
"""
Plot form factors.
"""
import bornagain as ba
from bornagain import nanometer, degree
import bornplot2 as bp
import math
import inspect
det = bp.DetPars(400, -.25, .25, -.25, .25)
n = 3
results = []
edge = 30
title = 'E=30'
trafo = ba.RotationY(26.5651 * degree)
ff = ba.FormFactorTruncatedCube(edge * nanometer, 2 * nanometer)
sim = bp.get_simulation(det, ff, trafo)
data = bp.run_sim(sim, det)
results.append(bp.Result(0, data, title))
pool = ff.getParameterPool()
print(pool.getParameterNames())
print(ff.getLength())
print(ff.volume())
pool.setParameterValue('Length', 10)
print(ff.getLength())
print(ff.volume())
title = 'E=10'
def get_sample():
# Defining Materials
material_1 = ba.HomogeneousMaterial("example01_Air", 0.0, 0.0)
material_2 = ba.HomogeneousMaterial("Si", 5.73327e-06, 1.006366e-07)
# Defining Layers
layer_1 = ba.Layer(material_1)
layer_2 = ba.Layer(material_2)
# Defining Form Factors
formFactor_1 = ba.FormFactorCone6(159.0 * nm, 10.0 * nm, 78.0 * deg)
formFactor_2 = ba.FormFactorCone6(159.0 * nm, 5.0 * nm, 66.0 * deg)
formFactor_3 = ba.FormFactorPrism6(159.0 * nm, 300.0 * nm)
particleComposition_11 = ba.ParticleComposition()
for i in range(nslices):
z = i * 15.0 * nm
y = z + 15.0 * nm
# Defining Particles
particle_1 = ba.Particle(material_2, formFactor_1)
particle_1_position = kvector_t(0.0 * nm, 0.0 * nm, z * nm)
particle_1.setPosition(particle_1_position)
particle_2 = ba.Particle(material_2, formFactor_2)
particle_2_rotation = ba.RotationY(180.0 * deg)
particle_2.setRotation(particle_2_rotation)
particle_2_position = kvector_t(0.0 * nm, 0.0 * nm, y * nm)
particle_2.setPosition(particle_2_position)
particleComposition_11.addParticle(particle_1)
particleComposition_11.addParticle(particle_2)
particleComposition_11_rotation = ba.RotationZ(j * deg)
particleComposition_11.setRotation(particleComposition_11_rotation)
particle_3 = ba.Particle(material_2, formFactor_3)
particle_3_rotation = ba.RotationY(30.0 * deg)
particle_3.setRotation(particle_3_rotation)
particle_3_position = kvector_t(0.0 * nm, 0.0 * nm, 79.5 * nm)
particle_3.setPosition(particle_3_position)
z1 = j
z2 = j + 120
z3 = j + 240
particleComposition_1 = ba.ParticleComposition()
particleComposition_1.addParticle(particle_3)
particleComposition_1_rotation = ba.RotationZ(z1 * deg)
particleComposition_1.setRotation(particleComposition_1_rotation)
particleComposition_2 = ba.ParticleComposition()
particleComposition_2.addParticle(particle_3)
particleComposition_2_rotation = ba.RotationZ(z2 * deg)
particleComposition_2.setRotation(particleComposition_2_rotation)
particleComposition_3 = ba.ParticleComposition()
particleComposition_3.addParticle(particle_3)
particleComposition_3_rotation = ba.RotationZ(z3 * deg)
particleComposition_3.setRotation(particleComposition_3_rotation)
# Defining Particle Layouts and adding Particles
layout_1 = ba.ParticleLayout()
layout_1.addParticle(particleComposition_11, 0.7)
layout_1.addParticle(particleComposition_1, 0.1)
layout_1.addParticle(particleComposition_2, 0.1)
layout_1.addParticle(particleComposition_3, 0.1)
layout_1.setTotalParticleSurfaceDensity(0.001)
# Adding layouts to layers
layer_1.addLayout(layout_1)
# Defining Multilayers
multiLayer_1 = ba.MultiLayer()
multiLayer_1.addLayer(layer_1)
multiLayer_1.addLayer(layer_2)
return multiLayer_1
